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https://www.readbyqxmd.com/read/27898297/a-novel-pfib-sample-preparation-protocol-for-correlative-3d-x-ray-cnt-and-fib-tof-sims-tomography
#1
Agnieszka Priebe, Guillaume Audoit, Jean-Paul Barnes
We present a novel sample preparation method that allows correlative 3D X-ray Computed Nano-Tomography (CNT) and Focused Ion Beam Time-Of-Flight Secondary Ion Mass Spectrometry (FIB-TOF-SIMS) tomography to be performed on the same sample. In addition, our invention ensures that samples stay unmodified structurally and chemically between the subsequent experiments. The main principle is based on modifying the topography of the X-ray CNT experimental setup before FIB-TOF-SIMS measurements by incorporating a square washer around the sample...
November 19, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/27873269/the-use-of-3d-telomere-fish-for-the-characterization-of-the-nuclear-architecture-in-ebv-positive-hodgkin-s-lymphoma
#2
Hans Knecht, Sabine Mai
The 3D nuclear architecture is closely related to cellular functions and chromosomes are organized in distinct territories. Quantitative 3D telomere FISH analysis (3D Q-FISH) and 3D super-resolution imaging (3D-SIM) at a resolution up to 80 nm as well as the recently developed combined quantitative 3D TRF2-telomere immune FISH technique (3D TRF2/Telo-Q-FISH) have substantially contributed to elucidate molecular pathogenic mechanisms of hematological diseases. Here we report the methods we applied to uncover major molecular steps involved in the pathogenesis of EBV-associated Hodgkin's lymphoma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27856800/normal-testes-asymmetry-evaluated-by-apparent-diffusion-coefficient-and-magnetization-transfer-ratio
#3
Athina C Tsili, Alexandra Ntorkou, Dimitrios Giannakis, Nikolaos Sofikitis, Maria I Argyropoulou
BACKGROUND: In humans, the left testis generally hangs lower than the right and the right is larger than the left. Magnetic resonance imaging (MRI) represents an important adjuvant modality in the investigation of testicular diseases. PURPOSE: To assess if normal testes asymmetry is related to apparent diffusion coefficient (ADC) and magnetization transfer ratio (MTR). MATERIAL AND METHODS: The normal testes from 106 men were included. Testicular volume (TV) was calculated by using the ellipsoid formula: length × width × height × 0...
November 17, 2016: Acta Radiologica
https://www.readbyqxmd.com/read/27826080/super-resolution-for-everybody-an-image-processing-workflow-to-obtain-high-resolution-images-with-a-standard-confocal-microscope
#4
France Lam, Damien Cladière, Cyndélia Guillaume, Katja Wassmann, Susanne Bolte
In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure...
November 5, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27794119/nanometer-scale-chemistry-of-a-calcite-biomineralization-template-implications-for-skeletal-composition-and-nucleation
#5
Oscar Branson, Elisa A Bonnin, Daniel E Perea, Howard J Spero, Zihua Zhu, Maria Winters, Bärbel Hönisch, Ann D Russell, Jennifer S Fehrenbacher, Alexander C Gagnon
Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27768294/understanding-the-magnetic-anisotropy-toward-single-ion-magnets
#6
Yin-Shan Meng, Shang-Da Jiang, Bing-Wu Wang, Song Gao
Single-molecule magnets (SMMs) can retain their magnetization status preferentially after removal of the magnetic field below a certain temperature. The unique property, magnetic bistable status, enables the molecule-scale SMM to become the next-generation high-density information storage medium. SMMs' new applications are also involved in high-speed quantum computation and molecular spintronics. The development of coordination chemistry, especially in transition metal (3d) and lanthanide (4f) complexes, diversifies SMMs by introducing new ones...
October 21, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27766219/osteogenic-odontogenic-bioengineering-with-co-administration-of-simvastatin-and-hydroxyapatite-on-poly-caprolactone-based-nanofibrous-scaffold
#7
Mohammad Samiei, Marziyeh Aghazadeh, Effat Alizadeh, Naser Aslaminabadi, Soodabeh Davaran, Sajjad Shirazi, Farhad Ashrafi, Roya Salehi
Purpose: Statin is an effective factor for promoting osteogenesis. The aim of the present study was to evaluate the effect of simvastatin (SIM) and/or HA addition on changes in osteogenesis levels by human DPSCs transferred onto three-dimensional (3D) nanofibrous Poly (ε-caprolactone) (PCL)/Poly lactic acide (PLLA) polymeric scaffolds. Methods: For this purpose, a 3D nanofibrous composite scaffold of PCL/PLLA/HA was prepared by electrospinning method. SIM was added to scaffolds during DPSCs culturing step...
September 2016: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/27753523/golgi-proteins-in-circulating-human-platelets-are-distributed-across-non-stacked-scattered-structures
#8
Shilpi Yadav, Jonathan K Williamson, Maria A Aronova, Andrew A Prince, Irina D Pokrovskaya, Richard D Leapman, Brian Storrie
Platelets are small, anucleate cell fragments that are central to hemostasis, thrombosis, and inflammation. They are derived from megakaryocytes from which they inherit their organelles. As platelets can synthesize proteins and contain many of the enzymes of the secretory pathway, one might expect all mature human platelets to contain a stacked Golgi apparatus, the central organelle of the secretory pathway. By thin section electron microscopy, stacked membranes resembling the stacked Golgi compartment in megakaryocytes and other nucleated cells can be detected in both proplatelets and platelets...
October 18, 2016: Platelets
https://www.readbyqxmd.com/read/27748959/study-of-ethanol-induced-golgi-disorganization-reveals-the-potential-mechanism-of-alcohol-impaired-n-glycosylation
#9
Carol A Casey, Ganapati Bhat, Melissa S Holzapfel, Armen Petrosyan
BACKGROUND: It is known that ethanol (EtOH) and its metabolites have a negative effect on protein glycosylation. The fragmentation of the Golgi apparatus induced by alteration of the structure of largest Golgi matrix protein, giantin, is the major consequence of damaging effects of EtOH-metabolism on the Golgi; however, the link between this and abnormal glycosylation remains unknown. Because previously we have shown that Golgi morphology dictates glycosylation, we examined the effect EtOH administration has on function of Golgi residential enzymes involved in N-glycosylation...
December 2016: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/27730644/scapular-flap-for-maxillectomy-defect-reconstruction-and-preliminary-results-using-three-dimensional-modeling
#10
Mara C Modest, Eric J Moore, Kathryn M Van Abel, Jeffrey R Janus, John R Sims, Daniel L Price, Kerry D Olsen
OBJECTIVES/HYPOTHESIS: Discuss current techniques utilizing the scapular tip and subscapular system for free tissue reconstruction of maxillary defects and highlight the impact of medical modeling on these techniques with a case series. STUDY DESIGN: Case review series at an academic hospital of patients undergoing maxillectomy + thoracodorsal scapula composite free flap (TSCF) reconstruction. Three-dimensional (3D) models were used in the last five cases. METHODS: 3D modeling, surgical, functional, and aesthetic outcomes were reviewed...
October 12, 2016: Laryngoscope
https://www.readbyqxmd.com/read/27730458/novel-application-of-3d-printing-in-brachytherapy-using-med610-3d-printed-insert-for-i-125-ropes-eye-plaque
#11
L Sim
The purpose of this study was to evaluate if MED610 3D printed material can be used as a surrogate for acrylic in the manufacturing of a replacement insert used in an eye plaque brachytherapy applicator. Measurement of the dose distributions from a standard acrylic insert were compared with dose obtained from MED610 3D printed replica using GafChromic(®) EBT3 films. The study used a 15 mm Radiation Oncology Physics and Engineering Services, Australia (ROPES) type eye plaque applicator loaded with I-125 (model 6711) seeds...
October 11, 2016: Australasian Physical & Engineering Sciences in Medicine
https://www.readbyqxmd.com/read/27726375/semi-empirical-rules-to-determine-drug-sensitivity-and-ionization-efficiency-in-sims-using-a-model-tissue-sample
#12
Jean-Luc Vorng, Anna M Kotowska, Melissa K Passarelli, Andrew West, Peter S Marshall, Rasmus Havelund, Martin P Seah, Colin T Dollery, Paulina D Rakowska, Ian S Gilmore
There is an increasing need in the pharmaceutical industry to reduce drug failure at late stage and so reduce the cost of developing a new medicine. Since most drug targets are intracellular this requires a better understanding of the drug disposition within a cell. Secondary ion mass spectrometry has been identified as a potentially important technique to do this as it is label-free and allows imaging in 3D with sub-cellular resolution and recent studies have shown promise for amiodarone. An important analytical parameter is sensitivity and we measure this in a bovine liver homogenate reference sample for twenty drugs representing important class-types relevant to the pharmaceutical industry...
October 11, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27722366/differential-regulation-of-nsc-phenotype-and-genotype-by-chronically-activated-microglia-within-cocultures
#13
Kurt Farrell, Ali Borazjani, Margot Damaser, Chandrasekhar R Kothapalli
Under disease or injury conditions in the central nervous system (CNS), activated microglia release cytokines and chemokines to modulate the microenvironment and influence tissue remodeling. To exploit the full potential of neural stem cell (NSC) transplantation approaches, a permissive microenvironment needs to be created for their survival, homing and differentiation. To investigate the role of chronically activated microglia in the fate of NSCs, spontaneously immortalized murine microglial cells (SIM-A9) were cocultured with embryonic murine cortical NSCs on 2D substrates or within 3D gels...
October 10, 2016: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/27683037/interaction-of-microtubules-with-the-actin-cytoskeleton-via-cross-talk-of-eb1-containing-tips-and-%C3%AE-actin-in-epithelial-cells
#14
Vera Dugina, Irina Alieva, Natalya Khromova, Igor Kireev, Peter W Gunning, Pavel Kopnin
Actin microfilaments and microtubules are both highly dynamic cytoskeleton components implicated in a wide range of intracellular processes as well as cell-cell and cell-substrate interactions. The interactions of actin filaments with the microtubule system play an important role in the assembly and maintenance of 3D cell structure. Here we demonstrate that cytoplasmic actins are differentially distributed in relation to the microtubule system. LSM, 3D-SIM, proximity ligation assay (PLA) and co-immunoprecipitation methods applied in combination with selective depletion of β- or γ-cytoplasmic actins revealed a selective interaction between microtubules and γ-, but not β-cytoplasmic actin via the microtubule +TIPs protein EB1...
September 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27667291/mesoscopic-perovskite-light-emitting-diodes
#15
Alessandro Lorenzo Palma, Lucio Cinà, Yan Busby, Andrea Marsella, Antonio Agresti, Sara Pescetelli, Jean-Jacques Pireaux, Aldo Di Carlo
Solution-processed hybrid bromide perovskite light-emitting-diodes (PLEDs) represent an attractive alternative technology that would allow overcoming the well-known severe efficiency drop in the green spectrum related to conventional LEDs technologies. In this work, we report on the development and characterization of PLEDs fabricated using, for the first time, a mesostructured layout. Stability of PLEDs is a critical issue; remarkably, mesostructured PLEDs devices tested in ambient conditions and without encapsulation showed a lifetime well-above what previously reported with a planar heterojunction layout...
October 3, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/27665783/meiotic-cohesin-subunits-rad21l-and-rec8-are-positioned-at-distinct-regions-between-lateral-elements-and-transverse-filaments-in-the-synaptonemal-complex-of-mouse-spermatocytes
#16
Mei Rong, Atsushi Matsuda, Yasushi Hiraoka, Jibak Lee
Cohesins containing a meiosis-specific α-kleisin subunit, RAD21L or REC8, play roles in diverse aspects of meiotic chromosome dynamics including formation of axial elements (AEs), assembly of the synaptonemal complex (SC), recombination of homologous chromosomes, and cohesion of sister chromatids. However, the exact functions of individual α-kleisins remain to be elucidated. Here, we examined the localization of RAD21L and REC8 within the SC by super-resolution microscopy, 3D-SIM. We found that both RAD21L and REC8 were localized at the connection sites between lateral elements (LEs) and transverse filaments (TFs) of pachynema with RAD21L locating interior to REC8 sites...
September 26, 2016: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/27661947/motion-artefact-detection-in-structured-illumination-microscopy-for-live-cell-imaging
#17
Ronny Förster, Kai Wicker, Walter Müller, Aurélie Jost, Rainer Heintzmann
The reconstruction process of structured illumination microscopy (SIM) creates substantial artefacts if the specimen has moved during the acquisition. This reduces the applicability of SIM for live cell imaging, because these artefacts cannot always be recognized as such in the final image. A movement is not necessarily visible in the raw data, due to the varying excitation patterns and the photon noise. We present a method to detect motion by extracting and comparing two independent 3D wide-field images out of the standard SIM raw data without needing additional images...
September 19, 2016: Optics Express
https://www.readbyqxmd.com/read/27634929/topology-independent-comparison-of-rna-3d-structures-using-the-click-algorithm
#18
Minh N Nguyen, Adelene Y L Sim, Yue Wan, M S Madhusudhan, Chandra Verma
RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting...
September 14, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27582118/analysis-of-chemotherapeutic-drug-delivery-at-the-single-cell-level-using-3d-msi-tof-sims
#19
Quentin P Vanbellingen, Anthony Castellanos, Monica Rodriguez-Silva, Iru Paudel, Jeremy W Chambers, Francisco A Fernandez-Lima
In this work, we show the advantages of label-free, tridimensional mass spectrometry imaging using dual beam analysis (25 keV Bi3(+)) and depth profiling (20 keV with a distribution centered at Ar1500(+)) coupled to time of flight secondary ion mass spectrometry (3D-MSI-TOF-SIMS) for the study of A-172 human glioblastoma cell line treated with B-cell lymphoma 2 (Bcl-2) inhibitor ABT-737. The high spatial (~250 nm) and high mass resolution (m/Δm ~10,000) of TOF-SIMS permitted the localization and identification of the intact, unlabeled drug molecular ion (m/z 811...
December 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27531441/in-planta-localization-of-stilbenes-within-picea-abies-phloem
#20
Tuula Jyske, Katsushi Kuroda, Jussi-Petteri Suuronen, Andrey Pranovich, Sílvia Roig-Juan, Dan Aoki, Kazuhiko Fukushima
Phenolic stilbene glucosides (astringin, isorhapontin, and piceid) and their aglycons commonly accumulate in the phloem of Norway spruce (Picea abies). However, current knowledge about the localization and accumulation of stilbenes within plant tissues and cells remains limited. Here, we used an innovative combination of novel microanalytical techniques to evaluate stilbenes in a frozen-hydrated condition (i.e. in planta) and a freeze-dried condition across phloem tissues. Semiquantitative time-of-flight secondary ion-mass spectrometry imaging in planta revealed that stilbenes were localized in axial parenchyma cells...
October 2016: Plant Physiology
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